By performing a locus-by-locus test on each of the hundreds of thousands of SNPs in a moderate sample size, a large number of false positive findings are expected to be generated in addition to the expected small number of true positive results.
Interestingly, unlike the locus-by-locus tests of selection, no significant difference is observed in the estimation of recurrent hitchhiking parameters between models including short fragments of closely linked polymorphism data compared with simply sequencing coding regions as assessed by comparing the relative mean square error between models (results not shown).
To address the low power implicit in single-locus tests of rare genetic variants, many rare-variant association approaches attempt to accumulate information across a gene, often by taking linear combinations of single-locus contributions to a statistic.
Single locus, haplotype, and multi-locus tests of association were performed.
Because the majority of the loci that are recorded by high-throughput sequencing are rare, classical single locus tests for genetic association, e.g. Amitrage-trend test (Lange and Laird, 2002), do not provide sufficient power for the underlying analysis questions.
Although we analysed only one minisatellite locus, in contrast to others using up to eight loci (reviewed by Bouffler et al, 2006), it is worth noting that significance in multiple locus tests requires correction for the number of loci tested, whereas our result does not.
A majority of the discriminatory loci (17 of 25) did not overlap with outlier loci identified by explicit tests of selection and thus were inferred to be selectively neutral.
Of the 50 loci tested, 14 of the loci met our locus Bonferroni criteria and another 24 were nominally significant.
Neutrality was tested through FST comparisons: FST values[ 17] were calculated for all loci by a locus-by-locus analysis of molecular variance (AMOVA) using ARLEQUIN.
In a two-staged design using 99,241 individuals of European ancestry, we identified 20 genome-wide significant (p ≤ 5 × 10−8) loci by using joint tests of the SNP main effect and SNP-age interaction.
Locus-by-locus departure from Hardy Weinberg equilibrium was tested by determining significance of the inbreeding coefficient FIS (heterozygosity deficit), with 10 000 permutations in Arlequin.
